SMTL ID : 4c8o.1

Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 1 residues within 4Å: Chain A: R.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.21 SO4.2: 5 residues within 4Å: Chain A: Q.321, H.347, R.367, K.371, F.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.321 Water bridges: A:Q.321 Salt bridges: A:H.347, A:K.371 SO4.5: 6 residues within 4Å: Chain A: F.17, V.18, L.19, K.22, W.106, R.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.19, A:L.19 Water bridges: A:W.106 Salt bridges: A:R.113 SO4.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.7: 5 residues within 4Å: Chain A: S.382, A.383, H.384, Y.394, Q.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.383, A:H.384 SO4.8: 3 residues within 4Å: Chain A: W.125, R.139, R.143 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.139, A:R.143 SO4.9: 3 residues within 4Å: Chain A: R.101, Y.102, R.127 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Y.102, A:Y.102, A:R.127 Salt bridges: A:R.101, A:R.127

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: R.21, K.22 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.10: 7 residues within 4Å: Chain B: A.4, C.5, G.6 Chain C: G.7, C.8, C.9, G.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Betz, K. et al., Structural Insights Into DNA Replication without Hydrogen Bonds. J.Am.Chem.Soc. (2013)

Release Date

2013-12-11

Peptides

DNA POLYMERASE I, THERMOSTABLE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA POLYMERASE I, THERMOSTABLE

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